Various techniques for analyzing biomolecules, such as polynucleotides or proteins, rely on the deposition of an array of particles, each attached to such biomolecules. Exemplary sequencing techniques rely on the deposition of an array of particles including a polynucleotide or copies thereof in an array of wells. In a particular example, the particles or beads can be deposited within the wells to associate the particles or beads with a particular sensor and to provide a local environment in which to analyze the biomolecules. In other examples, an ordered array of particles are deposited on a surface and analyzed without the benefit of wells.
There is a challenge to load samples on a surface in an organized manner, such that each sample does not interfere with another sample on the same surface. There is also a challenge to load closely spaced samples on a surface to form an array. It is desirable to create such arrays for nucleic acid or protein experimentation. In particular, it is desirable to create high-density arrays suitable for sequencing of genomes or for sequencing of low-frequency and rare variant mutations. It would also be desirable to place nucleic acids and in particular, nucleic acids bound to a delivery particle in an organized, tightly packed fashion, for example, to increase sequencing throughput per cycle, to lower customer cost per sequenced base, to run multiple samples in tandem, or to lower the overall amount of reagents used to generate sequencing information from an array. However, as nucleic acid deposition density (or nucleic acid-containing particle density) is increased the likelihood of nucleic acid clumping and nucleic acid stacking on a surface can also increase. Additionally, less than optimal loading conditions can result in one or more nucleic acids (or nucleic acid containing particles) entering the same location on the surface, such as a well, channel, pore or groove, and interfering with downstream data processing. Controlled organization of nucleic acids proteins, or particles and improved loading thereof can also simplify software identification of the nucleic acids or proteins on an array. Unfortunately, when nucleic acids, particles or proteins are stacked or clumped on an array, there can be problems with interrogation for their individual sequence or reporter signals.
In sequencing using delivery particles coated with nucleic acids, the overall throughput in terms of nucleic acid bases sequenced per sequencing run can directly depend on the number of readable delivery particles coated with nucleic acids in a given interrogation area, and generally, the more the better. Additionally, the amount of genetic information processed per run is dependent on the amount of nucleic acid bases sequenced per delivery particle. When delivery particles coated with nucleic acids are dispensed randomly onto an array, a considerable amount of space on the array can be left open. Furthermore, some delivery particles coated with nucleic acids can settle on the array in overlapping fashion, settle among interstitial spaces or stacking with other particles coated with nucleic acids, which can cause difficulties in resolving and interpreting images, signals or sequences of the nucleic acids bound to the delivery particles.
When processing an array containing particles coated with nucleic acids, it can be desirable to have the particles coated with nucleic acids packed as densely as possible to achieve the highest possible throughput. For example, when sequencing particles that include nucleic acids, it can be desirable to have a single nucleic acid sequence at one location on the array, for example, a reaction chamber, and for those locations to be present at a high-density to ensure high sequencing throughput. However, issues may arise for particles coated with nucleic acids such that the ionic field, diffraction circles or spread function is relatively large compared to the actual size of the particles coated with nucleic acids. Packing the particles coated with nucleic acids at a density such that the nucleic acid coated particles are all or mostly all touching each other can result in un-resolvable features, whether these coated particles are randomly arrayed or ordered in a close pack. Thus, improved methods, compositions, systems, apparatuses and kits for depositing samples, particularly particulate samples, onto various array surfaces would be desirable. Improved sequencing throughput of arrays as a result of improved sample loading would be desirable.